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parameters_RotationScan.ini
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/
parameters_RotationScan.ini
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[INPUT_FILES]
EnzymePDB = <enzyme pdb> # input enzyme pdb file (*.pdb)
SubstratePDB = <substrate pdb> # input substrate pdb file (*.pdb)
[PARAMETERS]
JOB_Name = <job name> # Name of the job
EnzymePrefix = <enzyme prefix> # name of an enzyme used as suffix for output (eg. dot1L).
SubstratePrefix = <substrate prefix> # name of the substrate used as suffix for file output (eg. NCP).
Substrate_Reaction_Atom = <pdb chain id> <residue name> <residue number> <atom name> # eg. In "E LYS 79 NZ", chain id = E, residue name = LYS, residue number = 79 atom name = NZ
# This atom involve in enzymatic reaction.
Enzyme_Reaction_Atom = <pdb chain id> <cofactor name> <cofactor number> <atom name> # eg. In "K SAM 500 CE ", chain id = K, residue name = SAM, residue number = 500 atom name = CE
# This atom of cofactor involve in enzymatic reaction.
Enzyme_Scissile_Atom2 = <pdb chain id> <cofactor name> <cofactor number> <atom name> # eg. In "K SAM 500 SD", chain id = K, residue name = SAM,
# residue number = 500 atom name = SD
# it is the atom bonded to enzyme's cofactor's reacting atom
Resolution = <integer> # Resolution of a rotation scan. High resolution scans
# are computationally expensive. As the resolution increases, the number of elemental rotations increase exponentially.
# Trait-Bryan angles for roation in 3D
# Each rotation in a rotation scan constitutes 3 elemental rotations alpha, beta and gamma about x, y, and z-axes, respectively.
# A scan range of -180 to + 180 for alpha, -90 to +90 for beta and -180 to +180 for gamma covers all the space
# that an object under roation could explore in three-dimensions.
AlphaLower = <integer> # lower value of an elemental rotation angle (alpha) about x-axis
AlphaUpper = <integer> # upper value of an elemental rotation angle (alpha) about x-axis
BetaLower = <integer> # lower value of an elemental rotation angle (beta) about y-axis
BetaUpper = <integer> # upper value of an elemental rotation angle (beta) about y-axis
GammaLower = <integer> # lower value of an elemental rotation angle (gamma) about z-axis
GammaUpper = <integer> # upper value of an elemental rotation angle (gamma) about z-axis
VDW_Radii_Sum_RAs = <float> # is the sum of van der Waal's radii of two reacting atoms.
# e.g., in case of methyltransferase, it the sum of vdw radii of CE of SAM and NE of Lys of substrate.
# the vdw radii for atoms are taken from taken from Probe program
# ref: Probe program; DOI: 10.1006/jmbi.1998.2400
# 'atom': <vdw> = {'H': -2.0, 'C': 1.7, 'N': 1.625, 'O': 1.480, 'P': 1.871, 'S': 1.782}
VDW_Clash_Threshold = 0.4 # Atom overlap in Angstroms for assigning the clash between atoms. Default is 0.4 according to Probe program
WriteOut_transformed_PDBs = false # TRUE or FALSE; whether to write pdb files from the roation scan or not.